# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 21:32:31 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 1-methyl-1'-(4-oxo-3,4,5,6,7,8-hexahydroquinazolin-2-yl)spiro[indole-3,4'-piperidin]-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C2(CCN(CC2)C3=NC4=C(CCCC4)C(=O)N3)c5ccccc15
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 9H6  9H6  1-methyl-1'-(4-oxo-3,4,5,6,7,8-hexahydroquinazolin-2-yl)spiro[indole-3,4'-piperidin]-2(1H)-one  ligand  51  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9H6
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 9H6  C10  C  CR5   0  -0.349   2.0336  -0.5197  -0.1947
 9H6  C11  C  CR5   0   0.594   3.1189  -1.5182  -0.6149
 9H6  C14  C  CH3   0  -0.542   5.5980  -1.5074  -0.8395
 9H6  C15  C  CR56  0   0.380   4.1929   0.4187  -0.1024
 9H6  C01  C  CH2   0  -0.476  -5.4361   0.9899   0.8827
 9H6  C02  C  CR6   0  -0.180  -4.1523   0.2806   0.5594
 9H6  C03  C  CR6   0   0.526  -3.6062  -0.6201   1.5316
 9H6  C06  C  CR6   0   0.756  -1.7950  -0.9956  -0.0363
 9H6  C08  C  CH2   0  -0.327   0.0471  -1.3813  -1.5551
 9H6  C09  C  CH2   0  -0.421   1.0532  -0.2561  -1.3561
 9H6  C16  C  CR16  0  -0.321   5.1847   1.3604   0.0986
 9H6  C17  C  CR16  0  -0.265   4.7904   2.6237   0.5382
 9H6  C18  C  CR16  0  -0.262   3.4537   2.9225   0.7633
 9H6  C19  C  CR16  0  -0.344   2.4699   1.9545   0.5518
 9H6  C20  C  CR56  0   0.151   2.8490   0.7022   0.1193
 9H6  C21  C  CH2   0  -0.413   1.2784  -1.0320   1.0483
 9H6  C22  C  CH2   0  -0.359   0.2664  -2.1249   0.7208
 9H6  C24  C  CR6   0   0.265  -3.4800   0.4334  -0.6221
 9H6  C25  C  CH2   0  -0.502  -3.9885   1.3522  -1.6952
 9H6  C26  C  CH2   0  -0.448  -5.4419   1.7580  -1.5001
 9H6  C27  C  CH2   0  -0.446  -5.6934   2.1623  -0.0551
 9H6  N05  N  NR16  0  -0.731  -2.4101  -1.2170   1.1540
 9H6  N07  N  NT    0  -0.488  -0.6528  -1.6720  -0.3125
 9H6  N13  N  NR5   0  -0.577   4.3297  -0.8974  -0.5314
 9H6  N23  N  N     0  -0.528  -2.3104  -0.1846  -0.9192
 9H6  O12  O  O     0  -0.454   2.9527  -2.6703  -0.9644
 9H6  H1   H  HCH3  0   0.255   6.0755  -1.0038  -1.6805
 9H6  H2   H  HCH3  0   0.255   6.2646  -1.4576   0.0213
 9H6  H3   H  HCH3  0   0.269   5.4416  -2.5500  -1.0992
 9H6  H4   H  HCH2  0   0.233  -6.2718   0.2836   0.8236
 9H6  H5   H  HCH2  0   0.240  -5.4160   1.3366   1.9187
 9H6  H6   H  HCH2  0   0.274  -0.6718  -1.1106  -2.3226
 9H6  H7   H  HCH2  0   0.265   0.5407  -2.2991  -1.8741
 9H6  H8   H  HCH2  0   0.255   0.5056   0.6647  -1.1394
 9H6  H9   H  HCH2  0   0.260   1.6049  -0.0800  -2.2825
 9H6  H10  H  HCR6  0   0.273   6.2289   1.1360  -0.0757
 9H6  H11  H  HCR6  0   0.259   5.5446   3.3815   0.7053
 9H6  H12  H  HCR6  0   0.255   3.1711   3.9097   1.1032
 9H6  H13  H  HCR6  0   0.253   1.4269   2.1916   0.7263
 9H6  H14  H  HCH2  0   0.265   1.9838  -1.3979   1.7976
 9H6  H15  H  HCH2  0   0.257   0.7506  -0.1884   1.5012
 9H6  H16  H  HCH2  0   0.277   0.7637  -3.0221   0.3538
 9H6  H17  H  HCH2  0   0.266  -0.2506  -2.4280   1.6289
 9H6  H18  H  HCH2  0   0.252  -3.3475   2.2408  -1.7023
 9H6  H19  H  HCH2  0   0.253  -3.8395   0.8717  -2.6647
 9H6  H20  H  HCH2  0   0.238  -5.6907   2.5740  -2.1810
 9H6  H21  H  HCH2  0   0.224  -6.0965   0.9214  -1.7637
 9H6  H22  H  HCH2  0   0.235  -6.7175   2.5179   0.0730
 9H6  H23  H  HCH2  0   0.221  -5.0362   2.9966   0.2096
 9H6  H24  H  HNR6  0   0.418  -2.0356  -1.8875   1.8102
 9H6  O04  O  O     0  -0.491  -4.0962  -0.8934   2.6213

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 9H6  C27  C01  single    1.523  0.020  1.523
 9H6  C27  C26  single    1.521  0.020  1.521
 9H6  C01  C02  single    1.502  0.020  1.502
 9H6  C26  C25  single    1.522  0.020  1.522
 9H6  O04  C03  double    1.226  0.020  1.226
 9H6  C02  C03  single    1.433  0.020  1.433
 9H6  C02  C24  double    1.368  0.020  1.368
 9H6  C03  N05  single    1.389  0.020  1.389
 9H6  C25  C24  single    1.501  0.020  1.501
 9H6  C24  N23  single    1.356  0.020  1.356
 9H6  N05  C06  single    1.358  0.020  1.358
 9H6  N23  C06  double    1.305  0.020  1.305
 9H6  C06  N07  single    1.356  0.020  1.356
 9H6  N07  C08  single    1.455  0.020  1.455
 9H6  N07  C22  single    1.455  0.020  1.455
 9H6  C08  C09  single    1.523  0.020  1.523
 9H6  C22  C21  single    1.525  0.020  1.525
 9H6  C09  C10  single    1.543  0.020  1.543
 9H6  C21  C10  single    1.542  0.020  1.542
 9H6  O12  C11  double    1.215  0.020  1.215
 9H6  C10  C11  single    1.533  0.020  1.533
 9H6  C10  C20  single    1.502  0.020  1.502
 9H6  C11  N13  single    1.363  0.020  1.363
 9H6  C20  C19  aromatic  1.378  0.020  1.378
 9H6  C20  C15  aromatic  1.391  0.020  1.391
 9H6  C19  C18  aromatic  1.396  0.020  1.396
 9H6  N13  C15  single    1.391  0.020  1.391
 9H6  N13  C14  single    1.441  0.020  1.441
 9H6  C15  C16  aromatic  1.382  0.020  1.382
 9H6  C18  C17  aromatic  1.388  0.020  1.388
 9H6  C16  C17  aromatic  1.395  0.020  1.395
 9H6  C14  H1   single    0.970  0.020  1.090
 9H6  C14  H2   single    0.970  0.020  1.090
 9H6  C14  H3   single    0.970  0.020  1.090
 9H6  C01  H4   single    0.970  0.020  1.090
 9H6  C01  H5   single    0.970  0.020  1.090
 9H6  C08  H6   single    0.970  0.020  1.090
 9H6  C08  H7   single    0.970  0.020  1.090
 9H6  C09  H8   single    0.970  0.020  1.090
 9H6  C09  H9   single    0.970  0.020  1.090
 9H6  C16  H10  single    0.930  0.020  1.080
 9H6  C17  H11  single    0.930  0.020  1.080
 9H6  C18  H12  single    0.930  0.020  1.080
 9H6  C19  H13  single    0.930  0.020  1.080
 9H6  C21  H14  single    0.970  0.020  1.090
 9H6  C21  H15  single    0.970  0.020  1.090
 9H6  C22  H16  single    0.970  0.020  1.090
 9H6  C22  H17  single    0.970  0.020  1.090
 9H6  C25  H18  single    0.970  0.020  1.090
 9H6  C25  H19  single    0.970  0.020  1.090
 9H6  C26  H20  single    0.970  0.020  1.090
 9H6  C26  H21  single    0.970  0.020  1.090
 9H6  C27  H22  single    0.970  0.020  1.090
 9H6  C27  H23  single    0.970  0.020  1.090
 9H6  N05  H24  single    0.860  0.020  1.020

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 9H6  C21  C10  C20  111.57  3.000
 9H6  C20  C10  C09  111.31  3.000
 9H6  C21  C10  C09  110.64  3.000
 9H6  C20  C10  C11  101.70  3.000
 9H6  C21  C10  C11  110.56  3.000
 9H6  C09  C10  C11  110.78  3.000
 9H6  O12  C11  N13  124.81  3.000
 9H6  N13  C11  C10  108.38  3.000
 9H6  O12  C11  C10  126.82  3.000
 9H6  H3   C14  H2   108.71  3.000
 9H6  H3   C14  H1   108.79  3.000
 9H6  H2   C14  H1   108.68  3.000
 9H6  H3   C14  N13  109.32  3.000
 9H6  H2   C14  N13  110.50  3.000
 9H6  H1   C14  N13  110.79  3.000
 9H6  N13  C15  C20  109.69  3.000
 9H6  N13  C15  C16  128.23  3.000
 9H6  C20  C15  C16  122.08  3.000
 9H6  H5   C01  H4   105.64  3.000
 9H6  H5   C01  C27  110.04  3.000
 9H6  H4   C01  C27  109.51  3.000
 9H6  H5   C01  C02  109.77  3.000
 9H6  H4   C01  C02  109.62  3.000
 9H6  C27  C01  C02  112.05  3.000
 9H6  C24  C02  C03  117.95  3.000
 9H6  C24  C02  C01  123.59  3.000
 9H6  C03  C02  C01  118.45  3.000
 9H6  O04  C03  N05  119.35  3.000
 9H6  N05  C03  C02  114.44  3.000
 9H6  O04  C03  C02  126.21  3.000
 9H6  N23  C06  N07  120.33  3.000
 9H6  N07  C06  N05  118.61  3.000
 9H6  N23  C06  N05  121.03  3.000
 9H6  H7   C08  H6   107.63  3.000
 9H6  H7   C08  N07  107.43  3.000
 9H6  H6   C08  N07  109.56  3.000
 9H6  H7   C08  C09  111.19  3.000
 9H6  H6   C08  C09  110.22  3.000
 9H6  N07  C08  C09  110.72  3.000
 9H6  H9   C09  H8   106.58  3.000
 9H6  H9   C09  C08  110.00  3.000
 9H6  H8   C09  C08  108.51  3.000
 9H6  H9   C09  C10  110.18  3.000
 9H6  H8   C09  C10  108.24  3.000
 9H6  C08  C09  C10  113.08  3.000
 9H6  H10  C16  C17  120.76  3.000
 9H6  H10  C16  C15  121.85  3.000
 9H6  C17  C16  C15  117.39  3.000
 9H6  H11  C17  C18  119.70  3.000
 9H6  H11  C17  C16  119.07  3.000
 9H6  C18  C17  C16  121.23  3.000
 9H6  H12  C18  C19  119.76  3.000
 9H6  H12  C18  C17  119.93  3.000
 9H6  C19  C18  C17  120.31  3.000
 9H6  H13  C19  C20  120.94  3.000
 9H6  H13  C19  C18  120.13  3.000
 9H6  C20  C19  C18  118.93  3.000
 9H6  C19  C20  C15  120.06  3.000
 9H6  C15  C20  C10  108.98  3.000
 9H6  C19  C20  C10  130.95  3.000
 9H6  H15  C21  H14  106.62  3.000
 9H6  H15  C21  C22  108.76  3.000
 9H6  H14  C21  C22  109.62  3.000
 9H6  H15  C21  C10  108.30  3.000
 9H6  H14  C21  C10  110.37  3.000
 9H6  C22  C21  C10  112.95  3.000
 9H6  H17  C22  H16  105.58  3.000
 9H6  H17  C22  N07  112.29  3.000
 9H6  H16  C22  N07  107.78  3.000
 9H6  H17  C22  C21  109.62  3.000
 9H6  H16  C22  C21  111.08  3.000
 9H6  N07  C22  C21  110.41  3.000
 9H6  N23  C24  C25  114.49  3.000
 9H6  N23  C24  C02  124.21  3.000
 9H6  C25  C24  C02  121.28  3.000
 9H6  H19  C25  H18  105.74  3.000
 9H6  H19  C25  C26  111.19  3.000
 9H6  H18  C25  C26  110.08  3.000
 9H6  H19  C25  C24  108.60  3.000
 9H6  H18  C25  C24  107.62  3.000
 9H6  C26  C25  C24  113.27  3.000
 9H6  H21  C26  H20  106.55  3.000
 9H6  H21  C26  C27  109.45  3.000
 9H6  H20  C26  C27  110.86  3.000
 9H6  H21  C26  C25  109.67  3.000
 9H6  H20  C26  C25  109.70  3.000
 9H6  C27  C26  C25  110.52  3.000
 9H6  H23  C27  H22  106.65  3.000
 9H6  H23  C27  C26  109.45  3.000
 9H6  H22  C27  C26  110.68  3.000
 9H6  H23  C27  C01  109.65  3.000
 9H6  H22  C27  C01  109.69  3.000
 9H6  C26  C27  C01  110.63  3.000
 9H6  H24  N05  C06  120.64  3.000
 9H6  H24  N05  C03  115.33  3.000
 9H6  C06  N05  C03  123.93  3.000
 9H6  C22  N07  C08  111.38  3.000
 9H6  C22  N07  C06  122.87  3.000
 9H6  C08  N07  C06  118.65  3.000
 9H6  C15  N13  C14  123.58  3.000
 9H6  C14  N13  C11  125.17  3.000
 9H6  C15  N13  C11  111.25  3.000
 9H6  C24  N23  C06  118.41  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 9H6  CONST_01  C18  C19  C20  C15     0.00   0.0  0
 9H6  CONST_02  C18  C17  C16  C15     0.00   0.0  0
 9H6  CONST_03  C19  C20  C15  C16     0.00   0.0  0
 9H6  CONST_04  C19  C18  C17  C16     0.00   0.0  0
 9H6  CONST_05  C20  C19  C18  C17     0.00   0.0  0
 9H6  CONST_06  C20  C15  C16  C17     0.00   0.0  0
 9H6  CONST_07  C15  N13  C11  C10     0.00   0.0  0
 9H6  CONST_08  C06  N05  C03  C02     0.00   0.0  0
 9H6  CONST_09  N23  C06  N05  C03     0.00   0.0  0
 9H6  CONST_10  N07  C06  N05  C03   180.00   0.0  0
 9H6  CONST_11  N05  C06  N07  C08   180.00   0.0  0
 9H6  CONST_12  N23  C06  N07  C08     0.00   0.0  0
 9H6  CONST_15  N05  C06  N23  C24     0.00   0.0  0
 9H6  CONST_16  N07  C06  N23  C24   180.00   0.0  0
 9H6  CONST_17  C14  N13  C11  C10   180.00   0.0  0
 9H6  CONST_18  O12  C11  N13  C15   180.00   0.0  0
 9H6  CONST_19  O04  C03  N05  C06   180.00   0.0  0
 9H6  CONST_20  H13  C19  C20  C10     0.00   0.0  0
 9H6  CONST_21  H11  C17  C16  C15   180.00   0.0  0
 9H6  CONST_22  H12  C18  C17  C16   180.00   0.0  0
 9H6  CONST_23  H10  C16  C17  C18   180.00   0.0  0
 9H6  CONST_24  H24  N05  C03  C02   180.00   0.0  0
 9H6  CONST_25  O12  C11  N13  C14     0.00   0.0  0
 9H6  Var_01    N07  C08  C09  C10    53.65  30.0  1
 9H6  Var_02    N07  C22  C21  C10   -54.40  30.0  1
 9H6  Var_03    C08  C09  C10  C11    77.34  30.0  3
 9H6  Var_04    C22  C21  C10  C11   -77.08  30.0  3
 9H6  Var_05    C09  C10  C20  C15  -117.78  30.0  1
 9H6  Var_06    C25  C26  C27  C01   -62.02  30.0  1
 9H6  Var_07    C26  C27  C01  C02    45.91  30.0  1
 9H6  Var_08    C26  C25  C24  C02   -15.78  30.0  1
 9H6  Var_09    C27  C01  C02  C03   164.89  30.0  1
 9H6  Var_10    C09  C08  N07  C06    89.42  30.0  1
 9H6  Var_11    C21  C22  N07  C06   -87.71  30.0  1
 9H6  Var_12    N13  C11  C10  C09   118.32  30.0  1
 9H6  Var_13    C27  C26  C25  C24    45.90  30.0  1
 9H6  Var_14    H1   C14  N13  C11   117.05  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 9H6  plan-1  C01  0.020
 9H6  plan-1  C02  0.020
 9H6  plan-1  C03  0.020
 9H6  plan-1  C06  0.020
 9H6  plan-1  C08  0.020
 9H6  plan-1  C22  0.020
 9H6  plan-1  C24  0.020
 9H6  plan-1  C25  0.020
 9H6  plan-1  N05  0.020
 9H6  plan-1  N07  0.020
 9H6  plan-1  N23  0.020
 9H6  plan-1  H24  0.020
 9H6  plan-1  O04  0.020
 9H6  plan-2  C10  0.020
 9H6  plan-2  C11  0.020
 9H6  plan-2  C14  0.020
 9H6  plan-2  C15  0.020
 9H6  plan-2  C16  0.020
 9H6  plan-2  C17  0.020
 9H6  plan-2  C18  0.020
 9H6  plan-2  C19  0.020
 9H6  plan-2  C20  0.020
 9H6  plan-2  N13  0.020
 9H6  plan-2  O12  0.020
 9H6  plan-2  H10  0.020
 9H6  plan-2  H11  0.020
 9H6  plan-2  H12  0.020
 9H6  plan-2  H13  0.020

